Yes, if you do auto-tune BEFORE the chuff adjustments, you won't affect them. But I personally have found that you can always get better results by manually setting CVs 51, 52, 53, 54, and 55 than using auto-tune. Yes, it takes significantly more time (and a lot of patience!) to do it this way, but the results in my cases have always been superior. And in any event, you should always do the chuff timing LAST, after you've finished with the BEMF settings, whether you use auto tune or do it manually.
John C.